options = Biopieces.options_parse(ARGV, casts)
-BASE_SOLEXA = 64
+ILLUMINA_BASE = 64
+ILLUMINA_MIN = 0
+ILLUMINA_MAX = 40
sum_hash = Hash.new(0)
count_hash = Hash.new(0)
if record[:SCORES]
scores = record[:SCORES]
(0 ... scores.length).each do |i|
- sum_hash[i] += (scores[i].ord - BASE_SOLEXA)
+ sum_hash[i] += (scores[i].ord - ILLUMINA_BASE)
count_hash[i] += 1
end
end
plot.ylabel options[:ylabel]
plot.output options[:data_out] if options[:data_out]
plot.xrange "[#{x.min - 1}:#{x.max + 1}]"
- plot.yrange "[0:40]"
+ plot.yrange "[#{ILLUMINA_MIN}:#{ILLUMINA_MAX}]"
plot.style "fill solid 0.5 border"
plot.xtics "out"
plot.ytics "out"